This ruling makes sense. The school was set up by the Bernice Pauahi Bishop Estate, with her designating native Hawaiians as the beneficiaries. I don't think it would be right for the government to alter the wishes of anyone's estate or trusts.
Try that with a white only school.
I remember reading about some guy who died in the early 60's and how his will was to go to some "Whites only" school. As I recall, the government stepped in and voided this provision based on discrimination.